Disclaimer: I can't draw a straight line, freehand, to save my life.

The GBA Cart Shape should be the basis for the main pre-cut-out area.
Just above it should be a piece of foam that's still connected to the main foam, at three points.
The three still-connected points are roughly indicated by the three arrows.
The end-user could use a pair of scissors to snip the three points, freeing that piece of foam, and remove it from the case, so that GB/GBC carts will fit.
You might want to also put a half-circle cutout on one side of the GBA Cart Area,
so people can get a finger in there, to leverage out the game cart.
You probably already have your own design in mind; this is only a suggestion.
EDITED TO ADD:Here's another idea.
This one has four cut-out points, instead of 3, and has the
half-circle cutouts, to make it easier to get the games out.
